
I am trying to analyze microarray data for a project where whole blood was collected from 4 different donors and was treated with a compound at 2 time-points at 4 different doses. I am interested in genes that are differentially regulated with dose, with time and also dose*time. When I run a PCA on the entire data, the separation of groups is mainly by donors. How do I run a limma analysis (factors, design matrix) to get to the genes of interest (mentioned earlier)? I am not interested in genes that are differentially expressed across donors. Any suggestion would be greatly appreciated.
 
Thanks,
Som.
 
Would it be O.K. to use ComBat to get rid off donor effects by treating each donor as a batch?
 
 
 

 
 		 	   		  
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